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- PDB-8blx: Engineered Fructosyl Peptide Oxidase - X02A mutant -

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Basic information

Entry
Database: PDB / ID: 8blx
TitleEngineered Fructosyl Peptide Oxidase - X02A mutant
ComponentsFructosyl Peptide Oxidase mutant (X02A)
KeywordsOXIDOREDUCTASE / FAD / Deglycating enzyme / Amadori product / Fructosyl Peptide Oxidase
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesParastagonospora nodorum SN15 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsEstiri, H. / Bhattacharya, S. / Rodriguez-Buitrago, J.A. / Parisini, E.
Funding support Latvia, 1items
OrganizationGrant numberCountry
Other governmentlzp-2020/2-0013 Latvia
CitationJournal: Sci Rep / Year: 2023
Title: Tailoring FPOX enzymes for enhanced stability and expanded substrate recognition.
Authors: Estiri, H. / Bhattacharya, S. / Buitrago, J.A.R. / Castagna, R. / Legzdina, L. / Casucci, G. / Ricci, A. / Parisini, E. / Gautieri, A.
History
DepositionNov 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fructosyl Peptide Oxidase mutant (X02A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,07712
Polymers47,2681
Non-polymers1,81011
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-9 kcal/mol
Surface area17530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.515, 130.258, 87.619
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Fructosyl Peptide Oxidase mutant (X02A)


Mass: 47267.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parastagonospora nodorum SN15 (fungus) / Strain: SN15 / ATCC MYA-4574 / FGSC 10173 / Gene: SNOG_08398 / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 20000 16-26%, MES 0.1M pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.918 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.71→56.682 Å / Num. obs: 55592 / % possible obs: 98.9 % / Redundancy: 11.5 % / CC1/2: 0.998 / Net I/σ(I): 12.7
Reflection shellResolution: 1.71→1.739 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 2685 / CC1/2: 0.461

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
autoPROCdata processing
Aimlessdata scaling
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y4J

6y4j


Resolution: 1.71→40.24 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.754 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21035 2833 5.1 %RANDOM
Rwork0.18116 ---
obs0.18262 52730 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.947 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-0 Å20 Å2
2--1.47 Å20 Å2
3----0.99 Å2
Refinement stepCycle: 1 / Resolution: 1.71→40.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3448 0 0 315 3763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123568
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163205
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.6474847
X-RAY DIFFRACTIONr_angle_other_deg0.5481.5727493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2175438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.045521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98410565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024011
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02716
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4622.6961713
X-RAY DIFFRACTIONr_mcbond_other2.4452.6961713
X-RAY DIFFRACTIONr_mcangle_it3.6594.0362143
X-RAY DIFFRACTIONr_mcangle_other3.6584.0362144
X-RAY DIFFRACTIONr_scbond_it3.43.1311855
X-RAY DIFFRACTIONr_scbond_other3.3973.131853
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1284.5072698
X-RAY DIFFRACTIONr_long_range_B_refined7.54638.4094234
X-RAY DIFFRACTIONr_long_range_B_other7.45236.7584149
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.71→1.754 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 193 -
Rwork0.317 3733 -
obs--96.37 %

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